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Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.)

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Abstract

Rice (Oryza sativa L.) yield enhancement is one of the prime objectives of plant breeders. Elucidation of the inheritance of grain weight, a key yield component trait, is of paramount importance for raising the yield thresholds in rice. In the present investigation, we employed Next-Generation Sequencing based QTL-seq approach to identify major genomic regions associated with grain weight using mapping populations derived from a cross between BPT5204 and MTU3626. QTL-seq analysis identified three grain weight quantitative trait loci (QTL) viz., qGW1 (35–40 Mb), qGW7 (10–18 Mb), and qGW8 (2–5 Mb) on chromosomes 1, 7 and 8, respectively and all are found to be novel. Further, qGW8 was confirmed through conventional QTL mapping in F2, F3 and BC1F2 populations and found to explain the phenotypic variance of 17.88%, 16.70% and 15.00%, respectively, indicating a major QTL for grain weight. Based on previous reports, two candidate genes in the qGW8 QTL were predicted i.e., LOC_Os08g01490 (Cytochrome P450), and LOC_Os08g01680 (WD domain, G-beta repeat domain containing protein) and through in silico analysis they were found to be highly expressed in reproductive organs during different stages of grain development. Here, we have demonstrated that QTL-seq is one of the rapid approaches to uncover novel QTLs controlling complex traits. The candidate genes identified in the present study undoubtedly enhance our understanding of the mechanism and inheritance of the grain weight. These candidate genes can be exploited for yield enhancement after confirmation through complementary studies.

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Abbreviations

SM:

Samba Mahsuri

HGW:

High grain weight

QTLs:

Quantitative trait loci

NGS:

Next generation sequencing

NGM:

Next generation mapping

BSA:

Bulked segregant analysis

SNP:

Single nucleotide polymorphism

QTLs:

Quantitative trait loci

TGW:

Thousand grain weight

ANOVA:

Analysis of variance

RAP-DB:

Rice annotation project-database

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Acknowledgements

BRY is grateful to the Institute of Frontier Technology and S.V. Agricultural College, Tirupati, ANGRAU for providing the facilities to conduct the experiment.

Funding

LRV is grateful to the Department of Biotechnology, Government of India for providing financial assistance [DBT-NER/AGRI/29/2015(GROUP- 4) dated 19/10/2016].

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Author notes

  1. Reddyyamini Bommisetty and Navajeet Chakravartty are contributed as first authors.

Authors and Affiliations

  1. Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India

    Reddyyamini Bommisetty, S. J. Mallikarjuna, G. R. Eswar, Gopalakrishna M. Kadambari, K. Hariprasadreddy, P. Rameshbabu & Lakshminarayana R. Vemireddy

  2. AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India

    Navajeet Chakravartty, Reddaiah Bodanapu, Sivarama P. Lekkala, Krishna Lalam, George Thomas, Saurabh Gupta & V. B. R. Lachagari

  3. Regional Agricultural Research Station, ANGRAU, Tirupati, 517502, India

    Jeevula B. Naik, Swarajyalakshmi N. Bollineni, Keerthi Issa & Srividhya Akkareddy

  4. Central University of Rajasthan, Ajmer, Rajasthan, India

    Sanjib K. Panda

  5. Agricultural Research Station, ANGRAU, Nellore, India

    C. Srilakshmi

  6. Department of Crop Physiology, S.V Agricultural College, ANGRAU, Tirupati, 517502, India

    P. Sudhakar

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  1. Reddyyamini Bommisetty
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  2. Navajeet Chakravartty
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Contributions

BRY, LRV and HKR planned the experiment. BRY and LRV contributed to the development of mapping populations. BRY performed the field experiments. JBN, BMM, EGR, GK, SBN and KI helped in phenotyping. SA, SC, RP and SP provided required materials and helped in maintaining the experiment. NC, RB, VBRL and SG sequenced the parents and bulks. NC, VBRL analysed the QTL-seq data. BRY, LRV SG, VBRL, and NC wrote the manuscript. VBRL, GT, SG, PSK and SPL reviewed the manuscript. All authors read and approved the manuscript.

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Correspondence to V. B. R. Lachagari or Lakshminarayana R. Vemireddy.

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Bommisetty, R., Chakravartty, N., Bodanapu, R. et al. Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.). Mol Biol Rep 47, 8615–8627 (2020). https://doi.org/10.1007/s11033-020-05904-7

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